How to determine the noncovalent binding peptides (hexamer)by MS?

[txqian]

Hi, there

How to determine the noncovalent binding peptides (hexamer of 34mer and 36mer peptides) by using mass spectrometry?

I am working on MS determination of noncovalent binding peptide (hexamer), but current instruments (MicrOTOF-Q and Autoflex (III) MALDI-TOF/TOF instruments , Bruker Daltonios) can detect monomer and dimer of the peptide, what's problem with the MS parameters? Are these two instruments suitable for detecting hexamer of peptide?

Thank you very much!

[peppy]

Hello,

MALDI is a soft ionization MS but I have noticed the matrix, which protects the peptides, can have varying effects on the ionization and vaporization. You can try different matrices (CHCA, THAP, Ferulic acid). Also try different preparation techniques, like overlayer instead of sandwich matrix preparation. You can also try and increase the power of the laser. Lastly, if none of these work, then it is possible that the hexamer cannot become ionized and fly in MALDI-TOF; in which case I would suggest trying an LCMS (ESI) and start with low tip voltages. An alternative approach is analytical ultracentrifugation which gives you information about subunit stoichiometry. You might also want to post in the MS section for some real guru advice.

Good Luck!

-John